


John and Atlantis

by StarGoddess



Series: Shadow 'Verse [2]
Category: Stargate Atlantis, Stargate SG-1
Genre: (Sort-of) Prequel, 5+1 Things, Alternate Universe - Canon Divergence (Post Series), Canon-Typical Violence, F/M, Fluff and Crack, Gen, Major Original Character(s), Sentient Atlantis, Telepathic Bond, Wraith
Language: English
Status: Completed
Published: 2014-03-22
Updated: 2014-03-22
Packaged: 2018-01-16 13:35:36
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 6
Words: 1,177
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1349260
Author URL: https://archiveofourown.org/users/StarGoddess/pseuds/StarGoddess
Summary: <blockquote class="userstuff">
              <p>Five times that John doesn't admit he hears Atlantis speaking to him and the one time he does.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> Set in the Shadow 'Verse. Exactly what it says on the tin. 
> 
> I do not own any of the Stargate characters or terms, I merely borrow them for my own amusement.

**Notes for the Chapter:**

> References season 1, episode 1, 'Rising: Part 1'.

The first time John hears Atlantis’ voice, he’s walking through the still mostly-dark control room.  He’s looking around at the consoles and thinks to himself ‘I really hope they still work’.  As soon as he finishes the thought, the large hanging screen in front of him flickers to life, followed immediately by the consoles he's turned around to look at.  He feels a buzzing in the back of his brain, almost a contented humming, as he raises his hands and says quickly, “I didn’t touch anything.”  He barely registers whatever Weir’s response is because he hears a strange female voice in his mind.  The words aren’t spoken in English, but somehow, he understands them.

It’s a simple, joyful, elated, “Welcome home, child.”

McKay says something about the consoles and John manages an appropriately snarky response, then Colonel Sumner is calling on the radio for Dr. Weir to join him three levels down.  He follows Dr. Weir and the voice is all but forgotten as he discovers they're underwater. 


	2. Chapter 2

**Notes for the Chapter:**

> References season 1, episode 11, 'The Eye'.

The next time he hears Atlantis, it’s not really words, but anguished cries of urgency.  He pleads with McKay to give Teyla and Beckett the two extra minutes to get to the control room before activating lightning-powered shield.  They arrive and McKay starts tapping the keys on the laptop, lightning striking all over the City.  John hears the urgent wordless pleas for the shield to activate, Atlantis desperately wanting to save them and herself from the storm.  He looks over to Weir nervously to see if she has noticed his unusual discomfort, then to Beckett and McKay, wondering how neither of them could hear her cries.  Then McKay activates the shield and the wave of relief that Atlantis sends towards him is almost palpable.

He takes a few seconds to recover, then eager to change the subject before someone notices his trembling hands, he says, “I see you made a new friend, Teyla,” and the moment passes.


	3. Chapter 3

**Notes for the Chapter:**

> References season 1, episode 20, 'The Siege: Part 2'.

When he hears Atlantis’ voice again, he’s already used to her constant presence in the back of his mind, providing comfort and encouragement whenever he’s in need.  He’s sitting in the control chair when he hears Rodney tell Elizabeth over the radio that the Mark II generator is dead and he comes to a decision effortlessly.  He says, “So long, Rodney,” and jumps out of the chair, running towards the jumper bay.  Atlantis tries to talk him out of his plan, pleading with him to give his colleagues more time, and he tries to make her understand that this is necessary for them all to survive.  He starts up the stairs to the 'jumper bay, has a few quick words with Elizabeth, and says out-loud to Atlantis and Elizabeth both, “I have to do this and you know it.”

He takes the jumper up and just as it passes out of Atlantis, he feels reluctant gratitude and hears a soft, sorrow-filled, “Goodbye, my Once-Lost Son,” in a language he shouldn’t understand, but does anyway.


	4. Chapter 4

**Notes for the Chapter:**

> References season 2, episode 20, 'Allies'; season 3, episode 1, 'No Man's Land'; season 3, episode 2, 'Misbegotten'.

By the time John has his first argument with Atlantis, he’s accepted the fact that either no one else can hear her or no one wants to admit an alien City talks to them.  The argument occurs when Elizabeth agrees to let Michael’s Hive Queen into the City.  Atlantis is extremely unhappy with John for freely allowing the Wraith to walk her halls and makes her displeasure known by alternatively ignoring him completely and giving him migraines with her constant litany of words.  It only gets worse when he agrees to let Rodney go aboard the Hive ship.  Atlantis is furious that John would allow his best friend to do something so dangerous.

The Wraith inevitably betray them and John almost dies several times before they make it home.  When they finally get the Hive ship back to Atlantis, John puts off going back to the City as long as possible in order to avoid the ‘I told you so’ he knows he’s going to get from her.  He does eventually go back to the City and after some profuse apologizing on his part, Atlantis lets him off with only one, “I did inform you that this would happen,” before she forgives him completely.


	5. Chapter 5

**Notes for the Chapter:**

> References season 5, episode 20, 'Enemy at the Gate' and the first story in this series, entitled 'Chaos'.

After Beckett crash lands his City into the Pacific Ocean, and John freely admits now that she’s been his since he first set foot in her five years ago, Atlantis tells him where to find his waiting teammates.  He joins them on the balcony overlooking the Golden Gate Bridge and shares his sense of peace and contentment with Atlantis.  She speaks to him as he looks out to the bridge, telling him how much the planet has changed since the last time she was here, wondering how many descendants are now scattered across the planet’s surface.

John and Atlantis have many conversations over the next year, which he grudgingly admits might be the only thing keeping him from flipping out on everyone, as Rodney and Zelenka work diligently to repair her star drive.  Woolsey and O’Neill manage to convince the IOA that Atlantis should be sent back to Pegasus, if only because the large area in the Pacific Ocean still under naval quarantine is starting to draw attention.  Two days before Atlantis is scheduled to leave, John is having another of his private conversations with the City, only pretending to pay attention to whatever Rodney is ranting about, when she suddenly stops speaking, mid-sentence.  He feels her consciousness shift away from him for several long minutes before she returns, excitement clear.  

When John asks her what happened, she replies with an elated, “She has come home.”

At the staff meeting the next day, John meets a beautiful, bruised, blonde woman with the most compelling violet eyes he’s ever seen.


	6. Chapter 6

**Notes for the Chapter:**

> References epilogue of the first story in this series entitled 'Chaos'.

The first time John admits to being able to hear Atlantis’ voice is the first time he wakes up in EJ’s room and finds her standing in the shower, having a one-sided conversation with thin air as she washes her long hair.  They’ve only been dating, though both of them are loathe to use that term, for a couple months and it’s the first time they’ve spent an entire night together.  Their relationship is still new and developing, both of them still learning each other, so he hesitates a moment before clearing his throat and asking, “Emma, who are you talking to?”

EJ startles only slightly before she answers, “Atlantis.”

John is stunned and a little bit jealous because at this point, he assumed that Atlantis spoke only to him.  So, of course, the only response he can give is, “You can hear her too?” as he strips off his underwear and joins EJ in the shower.  EJ smiles indulgently at him, shakes her head, and says, “Don’t worry, John, you’re still her favorite,” as she pulls his naked body close to hers.  John feels Atlantis’ heartfelt agreement and warm affection in the back of his mind before her consciousness moves away to give them privacy as John dips his head to kiss EJ’s smile.

**Notes for the Chapter:**

> Just a bit of fun because I was bored. Thanks for reading!
> 
> Questions, comments, and kudos are always appreciated!

**Author's Note:**

> Check out my tumblr - truestargoddess- for Stargate related things!


End file.
